Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems.

Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.

Changes in plant community assembly from patchy degradation of grasslands and grazing by different-sized herbivores.

Grassland degradation caused by increases in livestock grazing threatens a variety of ecosystem services. Understanding changes in plant community assembly during the process of grassland degradation in the presence of grazing is important to help restore degraded grasslands worldwide but has received little attention thus far. The grassland degradation process is typified by heterogeneous degradation, that is, gradual formation of degraded patches (hereafter "patchy degradation"). Here, we experimentally examined the effects of herbivore grazing and patchy degradation on plant community assembly using nine pairs of non-degraded (intact) and patch-degraded (fragmented) grasslands subject to grazing by different-sized herbivores (i.e., NG, no grazing; SG, sheep grazing; CG, cattle grazing) over 4 years. Using a null-model approach, we estimated the relative magnitude of deterministic processes of community assembly by comparing the observed and expected ß-diversity. We found that in the absence of herbivore grazing, deterministic processes played a greater role in community assembly, regardless of whether patchy degradation had occurred. However, the deterministic processes resulted in plant communities being more spatially similar in non-degraded grasslands while being more dissimilar in patchy degraded grasslands. Compared with non-degraded grasslands, species with strong competitive abilities (i.e., Leymus chinensis) were less dominant in patchy degraded grasslands, indicating relaxed competition and a reduced role of species interactions over plant communities. Instead, patchy degradation added the role of environmental variables over plant communities. SG consistently promoted more stochastic plant community assembly in both non-degraded and patch-degraded grasslands, while CG promoted more stochastic plant community assembly only in the non-degraded state, having no effect in the patch-degraded state. Our study offers important insights into changes in plant community assembly during ongoing patch-degradation of grasslands, indicating the role of increased environmental filtering of soil and reduced species interactions in driving plant community dynamics with increasing grassland patchy degradation. We also uncovered an herbivore species-specific effect on plant community assembly during the process of grassland degradation, which will better inform and improve future grassland restoration planning efforts.

Regulation of open populations of a stream insect through larval density dependence.

In organisms with complex life cycles, the various stages occupy different habitats creating demographically open populations. The dynamics of these populations will depend on the occurrence and timing of stochastic influences relative to demographic density dependence, but understanding of these fundamentals, especially in the face of climate warming, has been hampered by the difficulty of empirical studies. Using a logically feasible organism, we conducted a replicated density-perturbation experiment to manipulate late-instar larvae of nine populations of a stream caddisfly, Zelandopsyche ingens, and measured the resulting abundance over 2 years covering the complete life cycle of one cohort to evaluate influences on dynamics. Negative density feedback occurred in the larval stage, and was sufficiently strong to counteract variation in abundance due to manipulation of larval density, adult caddis dispersal in the terrestrial environment as well as downstream drift of newly hatched and older larvae in the current. This supports theory indicating regulation of open populations must involve density dependence in local populations sufficient to offset variability associated with dispersal, especially during recruitment, and pinpoints the occurrence to late in the larval life cycle and driven by food resource abundance. There were large variations in adult, egg mass and early instar abundance that were not related to abundance in the previous stage, or the manipulation, pointing to large stochastic influences. Thus, the results also highlight the complementary nature of stochastic and deterministic influences on open populations. Such density dependence will enhance population persistence in situations where variable dispersal and transitioning between life stages frequently creates mismatches between abundance and the local availability of resources, such as might become more common with climate warming.

Soil microbial community assembly model in response to heavy metal pollution.

Heavy metal pollution affected the stability and function of soil ecosystem. The impact of heavy metals on soil microbial community and the interaction of microbial community has been widely studied, but little was known about the response of community assembly to the heavy metal pollution. In this study, we collected 30 soil samples from non (CON), moderately (CL) and severely (CH) contaminated fields. The prokaryotic community was studied using high-throughput Illumina sequencing of 16s rRNA gene amplicons, and community assembly were quantified using phylogenetic-bin-based null approach (iCAMP). Results showed that diversity and composition of both bacterial and archaeal community changed significantly in response to heavy metal pollution. The microbial community assembly tended to be more deterministic with the increase of heavy metal concentration. Among the assembly processes, the relative importance of homogeneous selection (deterministic process) increased significantly (increased by 16.2%), and the relative importance of drift and dispersal limitation (stochastic process) decreased significantly (decreased by 11.4% and 5.4%, respectively). The determinacy of bacterial and archaeal community assembly also increased with heavy metal stress, but the assembly models were different. The deterministic proportion of microorganisms tolerant to heavy metals, such as Thiobacillus, Euryarchaeota and Crenarchaeota (clustered in bin 32, bin59 and bin60, respectively) increased, while the stochastic proportion of microorganisms sensitive to heavy metals, such as Koribacteraceae (clustered in bin23) increased. Therefore, the heavy metal stress made the prokaryotic community be deterministic, however, the effects on the assembly process of different microbial groups differed obviously.

Bayesian characterization of uncertainty in species interaction strengths.

Considerable effort has been devoted to the estimation of species interaction strengths. This effort has focused primarily on statistical significance testing and obtaining point estimates of parameters that contribute to interaction strength magnitudes, leaving the characterization of uncertainty associated with those estimates unconsidered. We consider a means of characterizing the uncertainty of a generalist predator's interaction strengths by formulating an observational method for estimating a predator's prey-specific per capita attack rates as a Bayesian statistical model. This formulation permits the explicit incorporation of multiple sources of uncertainty. A key insight is the informative nature of several so-called non-informative priors that have been used in modeling the sparse data typical of predator feeding surveys. We introduce to ecology a new neutral prior and provide evidence for its superior performance. We use a case study to consider the attack rates in a New Zealand intertidal whelk predator, and we illustrate not only that Bayesian point estimates can be made to correspond with those obtained by frequentist approaches, but also that estimation uncertainty as described by 95% intervals is more useful and biologically realistic using the Bayesian method. In particular, unlike in bootstrap confidence intervals, the lower bounds of the Bayesian posterior intervals for attack rates do not include zero when a predator-prey interaction is in fact observed. We conclude that the Bayesian framework provides a straightforward, probabilistic characterization of interaction strength uncertainty, enabling future considerations of both the deterministic and stochastic drivers of interaction strength and their impact on food webs.

In simple but challenging search tasks, most errors are stochastic.

In visual search tasks in the lab and in the real world, people routinely miss targets that are clearly visible: so-called look but fail to see (LBFTS) errors. If search displays are shown to the same observer twice, we can ask about the probability of joint errors, where the target is missed both times. If errors are "deterministic," then the probability of a second error on the same display-given that the target was missed the first time-should be high. If errors are "stochastic," the probability of joint errors should be the product of the error rate for first and second appearances. Here, we report on two versions of a T among Ls search with somewhat degraded letters to make search more difficult. In Experiment 1, Ts could either appear amidst crowded "clumps" of Ls or more in isolation. Observers made more errors when the T was in a clump, but these errors were mainly stochastic. In Experiment 2, the task was made harder by making Ts and Ls more similar. Again, errors were predominantly stochastic. If other, socially important errors are also stochastic, this would suggest that "double reading," where two observers (human or otherwise) look at each stimulus, could reduce overall error rates.

Responses of microeukaryotic community structure to a Phaeocystis globosa bloom in a semi-enclosed subtropical bay.

The occurrence of Phaeocystis globosa, a harmful algal bloom species in Chinese coastal waters, has significant impacts on marine organisms and poses a threat to the safety of coastal nuclear power plants. Although previous studies have established a close association between P. globosa blooms and the bacterial community, the relationship between the microeukaryotic community and P. globosa blooms remains poorly understood. In this study, the variations in the microeukaryotic community resulting from a P. globosa bloom were analyzed using 18S rRNA gene amplicon sequencing. The results indicated that the diversity of the microeukaryotic community during the bloom phase was significantly higher than that during the dissipation phase. The microeukaryotic community compositions varied significantly between the two phases of the P. globosa bloom. During the bloom phase, the dominant microeukaryotic was Viridiplantae, which was then replaced by Dinoflagellata during the dissipation phase. Co-occurrence network analysis showed that the relationship among the microeukaryotic community during the bloom phase was more complex than that during the dissipation phase, and the keystone taxa varied as the bloom progressed. Additionally, microeukaryotic community assembly was primarily driven by stochastic processes during the bloom phase based on the ß-nearest taxon distance, whereas it was driven by both deterministic processes and stochastic processes during the dissipation phase. Overall, our findings provide novel insight into the mechanisms and interactions involved in microeukaryotic community dynamics in environments disturbed by P. globosa blooms.

Resilience of the slow component in timescale-separated synchronized oscillators.

Physiological networks are usually made of a large number of biological oscillators evolving on a multitude of different timescales. Phase oscillators are particularly useful in the modelling of the synchronization dynamics of such systems. If the coupling is strong enough compared to the heterogeneity of the internal parameters, synchronized states might emerge where phase oscillators start to behave coherently. Here, we focus on the case where synchronized oscillators are divided into a fast and a slow component so that the two subsets evolve on separated timescales. We assess the resilience of the slow component by, first, reducing the dynamics of the fast one using Mori-Zwanzig formalism. Second, we evaluate the variance of the phase deviations when the oscillators in the two components are subject to noise with possibly distinct correlation times. From the general expression for the variance, we consider specific network structures and show how the noise transmission between the fast and slow components is affected. Interestingly, we find that oscillators that are among the most robust when there is only a single timescale, might become the most vulnerable when the system undergoes a timescale separation. We also find that layered networks seem to be insensitive to such timescale separations.

Assembly of a Benthic Microbial Community in a Eutrophic Bay with a Long History of Oyster Culturing.

The introduction of oysters to a waterbody is an efficient method for decreasing levels of eutrophication. Oysters affect sedimental environments and benthic microbes via their roles in nutrient cycling. However, little is known about how long-term oyster culturing affects benthic microbial community assembly. In the present study, top and bottom sediments from an oyster-culture area and non-culture area, in a eutrophic bay with a long history of oyster culturing, were obtained for environmental parameter measurement and microbe identification. Deterministic and stochastic processes in microbial community assembly were assessed. In particular, keystone species identification through network analysis was combined with measured environmental parameters to determine the factors related to community assembly processes. Our results suggest that oyster culturing relates to greater variation in both biological and non-biological sediment profiles. In benthic communities, Proteobacteria and Chloroflexi were the most abundant phyla, and community compositions were significantly different between sample groups. We also found that community assembly was more affected by deterministic factors than stochastic ones, when oysters were present. Moisture, or water content, and pH were identified as affecting deterministic and stochastic processes, respectively, but only water content was a driver associated with oyster culturing. Additionally, although keystone species presented a similar pattern of composition to peripheral species, they responded to their environments differently. Furthermore, model selection, fitting keystone species to community assembly processes, indicates their role in shaping microbial communities.

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

BACKGROUND: Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks. RESULTS: The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa. CONCLUSIONS: These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions. Video abstract.

Instability and Uncertainty Are Critical for Psychotherapy: How the Therapeutic Alliance Opens Us Up.

Tschacher and Haken have recently applied a systems-based approach to modeling psychotherapy process in terms of potentially beneficial tendencies toward deterministic as well as chaotic forms of change in the client's behavioral, cognitive and affective experience during the course of therapy. A chaotic change process refers to a greater exploration of the states that a client can be in, and it may have a potential positive role to play in their development. A distinction is made between on the one hand, specific instances of instability which are due to techniques employed by the therapist, and on the other, a more general instability which is due to the therapeutic relationship, and a key, necessary result of a successful therapeutic alliance. Drawing on Friston's systems-based model of free energy minimization and predictive coding, it is proposed here that the increase in the instability of a client's functioning due to therapy can be conceptualized as a reduction in the precisions (certainty) with which the client's prior beliefs about themselves and their world, are held. It is shown how a good therapeutic alliance (characterized by successful interpersonal synchrony of the sort described by Friston and Frith) results in the emergence of a new hierarchical level in the client's generative model of themselves and their relationship with the world. The emergence of this new level of functioning permits the reduction of the precisions of the client's priors, which allows the client to 'open up': to experience thoughts, emotions and experiences they did not have before. It is proposed that this process is a necessary precursor to change due to psychotherapy. A good consilience can be found between this approach to understanding the role of the therapeutic alliance, and the role of epistemic trust in psychotherapy as described by Fonagy and Allison. It is suggested that beneficial forms of instability in clients are an underappreciated influence on psychotherapy process, and thoughts about the implications, as well as situations in which instability may not be beneficial (or potentially harmful) for therapy, are considered.

Extraneous E-Cadherin Engages the Deterministic Process of Somatic Reprogramming through Modulating STAT3 and Erk1/2 Activity.

Although several modes of reprogramming have been reported in different cell types during iPSC induction, the molecular mechanism regarding the selection of different modes of action is still mostly unknown. The present study examined the molecular events that participate in the selection of such processes at the onset of somatic reprogramming. The activity of STAT3 versus that of Erk1/2 reversibly determines the reprogramming mode entered; a lower activity ratio favors the deterministic process and vice versa. Additionally, extraneous E-cadherin facilitates the early events of somatic reprogramming, potentially by stabilizing the LIF/gp130 and EGFR/ErbB2 complexes to promote entry into the deterministic process. Our current findings demonstrated that manipulating the pSTAT3/pErk1/2 activity ratio in the surrounding milieu can drive different modes of action toward either the deterministic or the stochastic process in the context of OSKM-mediated somatic reprogramming.

Somatic Reprogramming-Above and Beyond Pluripotency.

Pluripotent stem cells, having long been considered the fountain of youth, have caught the attention of many researchers from diverse backgrounds due to their capacity for unlimited self-renewal and potential to differentiate into all cell types. Over the past 15 years, the advanced development of induced pluripotent stem cells (iPSCs) has displayed an unparalleled potential for regenerative medicine, cell-based therapies, modeling human diseases in culture, and drug discovery. The transcription factor quartet (Oct4, Sox2, Klf4, and c-Myc) reprograms highly differentiated somatic cells back to a pluripotent state recapitulated embryonic stem cells (ESCs) in different aspects, including gene expression profile, epigenetic signature, and functional pluripotency. With the prior fruitful studies in SCNT and cell fusion experiments, iPSC finds its place and implicates that the differentiated somatic epigenome retains plasticity for re-gaining the pluripotency and further stretchability to reach a totipotency-like state. These achievements have revolutionized the concept and created a new avenue in biomedical sciences for clinical applications. With the advent of 15 years' progress-making after iPSC discovery, this review is focused on how the current concept is established by revisiting those essential landmark studies and summarizing its current biomedical applications status to facilitate the new era entry of regenerative therapy.